All 2012 R2 boxes were fully patched before upgrading; ADFS was split out onto a seperate box as the upgrade is not capable of an in-place upgrade of this element - the process as documented here is fantastic for migrating this. I still haven't installed WSUS again but I'm planning on rebuilding the SCCM element of my lab anyway, so don't need it yet.

The only snag I've encountered is that when you do the in place upgrade for server core, you need to run Setup with a couple of parameters - /Compat IgnoreWarning - otherwise you just get a blue screen.

The Web Application Proxy server upgraded fine, but the WAP component was left in an invalid state; I just removed it and reinstalled as I was resetting ADFS anyway -- likewise Azure AD Connect needed to be reinstalled and reconnected.

Finally, a disk cleanup frees up space - just run dism.exe /online /Cleanup-Image /StartComponentCleanup /ResetBasealthough it should be noted this will prevent you reverting the upgrade etc.